Filtering and sorting of multiallelic sites

Question

[gernophil]

Hey everyone,

since splitting of multiallelic sites the way bcftools does it, doesn't really work for me, I am looking for a good way to sort and/or filter multiallelic sites by allele frequency.

bcftools view --min-af 0.05:alt1 will filter all variants of multiallelic sites with AF of ALT1 < 5% even, if ALT2 (or ALT3) would have a higher AF.

bcftools view --min-af 0.05:nref wil combine the AFs of all ALT alleles, which also isn't what I want to do.

Is there a good tool, that can filter all ALT alleles separately? Or is there a tool to sort all ALTs by their AF so I would at least have the most common at the beginning?

Thanks in advance